In recent years, with the rapid development of urban economy and water conservancy construction, the water environment in the Poyang Lake Basin has gradually deteriorated. Freshwater ecosystems are destroyed, soil erosion is intensified, lakes tend to be more tropical, and the risk of environmental pollution increases. The purpose of this paper is to study the structure of aquatic organism community and the ecological effect of environmental pollution in Poyang Lake. The ecological effects of aquatic biodiversity and environmental pollution are introduced. This paper summarizes the overall environmental status of the Poyang Lake Basin and puts forward the protection strategies of Poyang Lake aquatic organisms. Focus on analyzing the temporal and spatial dynamics of the zooplankton community structure in Poyang Lake, study the differences in community structure in different seasons and divide different types of communities, explore the factors that lead to differences in community structure, and analyze the main community structures. Environmental factors affecting zooplankton community structure. The water quality of Poyang Lake was evaluated by water physicochemical factors and biological indicators. The Shannon-Wiener diversity index and BI index evaluation results showed that the water body of sampling point 2 was seriously polluted, and most of the other water bodies were moderately or polluted.